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zhaoxiaofei / bindash

Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
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BinDash 2.0 usage and build? #21

Open jdwinkler opened 2 months ago

jdwinkler commented 2 months ago

Thanks for your work on BinDash! I am interested in using BinDash2.0 as a replacement for Mash. Is there a particular commit I should build to try it? If it is possible for you to provide an example of the output format, that would be great as well.

Thank you in advance!

jianshu93 commented 2 months ago

Hi @jdwinkler,

You can use the bioconda version if you do not want to build from source. But this repo is the most recent version and is consistent with the bioconda version. Output format is exact the same with Mash, commands would be like: 

### strep_small_name.txt is the query genome path (gz supported), sketch 188*64=12032, to be accurate at > 99.99% ANI
bindash sketch --kmerlen=16 --nthreads=32 --sketchsize64=188 --dens=2 --bbits=32 --minhashtype=2 --listfname=strep_small_name.txt --outfname=strep_small_k16_s500.bindash

### database_name.txt is the database genome path (gz supported)
bindash sketch --kmerlen=16 --nthreads=32 --sketchsize64=188 --dens=2 --bbits=32 --minhashtype=2 --listfname=database_name.txt --outfname=database.bindash

bindash dist --nthreads32 --outfname=S_bindash_new.txt strep_small_k16_s500.bindash database.bindash

Thank you for your interest in BinDash 1/2.

Jianshu & Xiaofei

jdwinkler commented 2 months ago

Thank you!